by Paul Braterman
Types of comment
Comments I have had from creationists fall into three broad groups (and note that contrary to what Dawkins says, some of these are at least partly informed, highly intelligent, and completely rational):
1) Simple misstatements
2) Appeal to the Bible
3) Purportedly scientific arguments, some without merit, while others refer to important issues.
From simple misstatements, not very much can be learnt, except perhaps the source of the misinformation. Remember that if someone quotes wrong information, the burden of proof is not on you but on them. Leave it there, as in this actual exchange:
Creationist: Chimps are not our relatives. The genomic similarity between humans and chimps is only 29.8%.
Me: "The genomic similarity between humans and chimps is only 29.8%"; if so, I have been seriously misinformed. Please give your source for this information.
I am of course being disingenuous. I do not really think that I have been seriously misinformed, and I could have cited the standard literature value of over 98%. But much better to leave the burden of proof where it belongs. Meantime, I have (truthfully) presented myself to bystanders as open to new information, if only the creationist would supply it (he didn't).
What about the Bible?
a) Denounce the Bible as the ignorant writings of bronze-age goatherds, or
b) Describe the Bible as the written and rewritten work of scribes and scholars, over many generations, doing their best with the knowledge they had at that time about how the world works, and constrained to express their beliefs in language that made sense to them and their contemporaries.
Which do you think is more likely to win new friends, and which, for that matter, is more accurate?
And now to science
A creationist favourite: mutation plus natural selection cannot generate new information, since mutation merely generates noise, and selection can eliminate, but not produce, novelty. My reply (and I found it instructive to have to formulate it), and how it led to a further informative exchange:
Me: You are right twice and wrong once about how evolution works. Correct; selection alone cannot create novelty. Correct; random mutation alone cannot create significance (and most mutations are harmful or at best neutral). But, as in the case of genetic algorithms, the combination of the two of them can indeed create meaningful novelty. [In computing, a genetic algorithm takes an initial computer program, allows it to mutate, compares the new program with its predecessor, keeps whichever is better on some pre-established criterion, and repeats.]
Creationist: Genetic algorithms are designed to reach specific pre-defined goals. Natural selection isn't.
Me: Natural selection has a very specific pre-defined goal. Survival.
The problem of complexity
Then, of course, the evolution of complex systems. The mammalian camera-like eye, with retina, lens, and pupil. This is an old creationist favourite, perhaps because Darwin himself said2 that "To suppose that the eye, with all its inimitable contrivances … could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree". We have, however, learnt quite a lot about this since 1859. Darwin went on to spell out all the things that we would need to show in order to explain the evolution of the eye by natural selection, and in this he has been fully vindicated.
Other multicomponent systems. Flowers and pollinators. Male and female. The blood clotting system. The bacterial flagellum. Parasites and their hosts.
Here I think we need to answer at three different levels. At the most general level, the creationist is claiming that because we don't know how something could arise by natural processes, it could only have arisen by supernatural intervention. Technically, this is known as the "argument from ignorance". In antiquity, it might have been used to prove the reality of the Sun God's chariot, and today it is routinely used to invoke a miraculous origin for life, or for the Universe, or for consciousness. It is a pernicious argument; because we haven't found an explanation within our current science, we are invited to stop looking.
Going down a step, all the arguments involve the assumption that the systems would not work unless all their parts were already in place. Well, perhaps they would not work so effectively, or in the same way, but to get the ball rolling they wouldn't need to. Good examples here are the blood clotting system, which involves the operation of a large number of successive steps in order to stop bleeding, and the bacterial flagellum, a kind of "motor" used by some bacteria to propel themselves, through the combined action of many different protein molecules. Both of these were produced, and both found wanting, as examples of irreducible complexity at Kitzmiller v Dover,3 where the critics of Intelligent Design creationism were able to point to numerous partial precursor systems. As the links cited here show, the family relationships between these are the subject of active ongoing research.
Finally, getting down to particulars, what the creationist is actually doing is setting out a series of excellent research programmes, many of them, as mentioned in the case of the flagellum, already vigorously under way. Life, alas, is short, and there is not time to satisfy all one's curiosities, but it is always instructive to have that curiosity aroused. My reading has certainly benefited from creationists' questions about the eye, the appearance of new species, random drift versus selection, whether evolution is the same thing as progress (it isn't4) and the evolution of parasites, some with extremely complex lifecycles involving several hosts. I am also left wondering how the creationists themselves explain the very existence of parasites, if they believe that every living kind was separately hand-crafted by a benign Deity.
R: Life cycle of heterophytids, parasites that use three separate hosts at different stages. Click to enlarge.
Deep time
Then there is geology, and the Young Earth creationist challenge to the deep time necessary for evolution. I was asked, for instance, why the Colorado had carved out a canyon, but mightier rivers such as the Nile and Amazon had not, and why the Nile delta wasn't much larger than it is if it had been in place for many millions of years. (What's your answer? Mine's at the end of this post. Good to be made to think about it, and more to it than I had realised).
And other alleged problems with the age of the Earth. The thickness of sediments suggests an age of "only" 100 million years, and if we divide the amount of salt in the oceans by the amount brought down by rivers each year, we get a similar number. So indeed 100 million years was the figure generally accepted by geologists at the end of the nineteenth century. But why do creationists keep talking about this? An Old Earth creationist has no reason to care, while a Young Earth creationist needs an age measured in at most thousands of years, so 100 million years is no better than the actual value of around 4.57 billion. No matter; conflicting claims have been made in the name of science, and so, by a lawyerly trick, we are invited to regard science in the same light as we would a witness who changed his story on the stand. The very opposite of the scientific attitude which (ideally at least) regards mistakes as both inevitable and instructive.
As to how geologists 120 years ago got it so badly wrong, it's worth noting that logically their suggestions were lower limits. They took into account how fast material (sediments on land, salt and the oceans) was arriving, but had no idea of how effectively it was being removed. They did not know about subduction, part of the process of plate tectonics, which returns sediments to the Earth's mantle beneath the crust. Nor did they realise the extent to which the continents had moved, cutting off regions as large as the Mediterranean basin and allowing them to evaporate to dryness, depositing their salt content.
Other old favourites
R: Macaque monkeys grooming 
Above, R: Archaeopteryx, the “Berlin specimen,” showing leg feathers later removed in cleaning. Click to enlarge. The 1863 specimen, referred to by Darwin, is in London’s Natural History Museum; its image is copyright but can be seen here.
But aren't there still missing links? Yes there are, and there always will be. And yes, just as the creationists say, filling in the gaps is an act of interpretation. Find an incomplete sequence of footprints in the sand at the edge of the ocean, and you can interpret them as evidence that someone walked that way. Or you can insist that each separate footprint was the result of a separate act of creation, and none can prove you wrong. The same is true for the hundreds of thousands of fossils, all at the right place in the geological sequence, unknown to Darwin, but known to us. The creationist cites the inescapable incompleteness of the record, but under creationism we would not expect any record at all.
And some other good questions
The creationists raised numerous other important questions, to which I will be returning in my own reading, and some of which may feature here at some future date. The Cambrian explosion (hint: "explosion" is a relative term). Not seeing evolution actually occurring (yes we do, actually, all the time). What did our last common ancestor with chimps look like? And how could our large difference from chimps be achieved with so little difference in our DNA? (Good questions, still largely unanswered). The origin of life; we don't know, lots of interesting work going on. Notice, though, that this isn't really a question about biological evolution itself, but about what had to happen before that evolution got started. Think of the chemists, who had spent 150 years using and developing atomic theory before we developed any insight into the origin of atoms.5 The distinction between historical and operational science (yes they are different, but not in the way people usually imagine. It is historical science that is the more certain!) Evolution doesn't explain consciousness, define morality, or give meaning and purpose to our lives (should we expect it to?) Are scientific statements the only rational ones? (My own heretical view: we can usefully ask whether a statement is rational, but I see nothing more to be learnt by then asking whether it is scientific.) No proof of evolution? A good jumping off point for thinking about what counts as "proof" in science. Or does science do proof at all? Much to think about here; much to learn from.
Those rivers again
Now what about those rivers? What about the Grand Canyon, and the absence of canyons for the Amazon and the Nile? The answers were pretty well what I had guessed, but with much more interesting detail. The Grand Canyon formed as a result of the uplifting of the Colorado Plateau by between 1,500 and 3,000 metres, and was further enlarged during the Ice Ages, when there was much heavier rainfall upstream. The so-called Eonile, precursor to the modern Nile, did indeed cut a deep canyon during the period, up to around five million years ago, when the Mediterranean was isolated from the Atlantic and dried up. So the expected massive sediments do indeed exist, but are now under water, and the canyon was formed, but has long since been filled in. The Amazon does indeed have a massive land delta, as well as underwater formations spreading up to 300 km from the coastline. The river in its present form is only some ten million years old, with its headwaters reshaped by the rise of the Andes. If so, by analogy with the Colorado you might expect it to have carved up a canyon in the area of uplift, and you would not be disappointed. The Rio Marañon, principal feeder to the Amazon, 
R: Strata bent by lateral compression in wall of Marañon canyon
Conclusion
With evolution, as with everything else, we are blind to our own confirmation bias. We will focus, if left to ourselves, on questions that are easily answered, and avoid those that might make us uncomfortable. But such questions are by far the most instructive, and we owe a debt of gratitude to those who raise them, whether they want our thanks or not.
Some useful resources
"29+ Evidences for Macroevolution" http://www.talkorigins.org/faqs/comdesc/ especially Prediction 4.5 and Figure 4.4.1 at http://www.talkorigins.org/faqs/comdesc/section4.html#retroviruses
Speciation: http://www.talkorigins.org/faqs/faq-speciation.html and http://www.talkorigins.org/faqs/speciation.html . "Lizards Undergo Rapid Evolution After Introduction To A New Home" https://www.sciencedaily.com/releases/2008/04/080417112433.htm
Human evolution; Smithsonian Institute, http://humanorigins.si.edu/evidence/human-fossils ; timeline of human fossil discoveries, https://australianmuseum.net.au/a-timeline-of-fossil-discoveries
Whale evolution: Thewissen's review article, free download, https://link.springer.com/article/10.1007/s12052-009-0135-2
The Cambrian Explosion http://www.geologypage.com/2017/08/mystery-first-animals-appeared-earth-solved.html Jochen J. Brocks, Amber J. M. Jarrett, Eva Sirantoine, Christian Hallmann, Yosuke Hoshino, Tharika Liyanage. The rise of algae in Cryogenian oceans and the emergence of animals. Nature, 2017
Historical vs operational science: https://pubs.geoscienceworld.org/books/book/667/chapter/3807501/Common-cause-explanation-and-the-search-for-a
1] Ben Zomah, Mishnah Aboth 4:1
2] Origin of Species, 1st ed., Ch 6, "Difficulties on Theory"
3] The 2005 court case establishing that Intelligent Design is merely a variant of religious creationism, and as such cannot be taught in government-run schools in the US.
4] The actual balance between selection, drift, and constraints in particular cases is a major research area. See e.g. my earlier Evolution is not progress
5] We can date the modern atomic theory to Dalton's New System of Chemical Philosophy, 1808, and our understanding of how atoms are formed to papers by Fred Hoyle and colleagues in the 1950s.
An earlier version of some of this material appeared in The Conversation.
Bible image from bible-png. Eye development image Matticus78 via Wikipedia. Sun God in chariot, Ilium (Troy), Temple of Athena, via Wikipedia. Falgellum and injectisome image Matt Baker. Parasite lifecylcle from CDC via Stanford. Monkeys grooming AKS.9955 via Wikipedia. Archaeopteryx, from Vogt, C. 1880, Archaeopteryx macrura, an Intermediate Form between Birds and Reptiles, Ibis 4:434-45, via Wikipedia. Hominin skulls from Smithsonian. Grand Canyon image Luca Galuzzi (who must be informed regarding re-use) via Wikipedia. Marañon Canyon © David O'Keefe, via https://community.nrs.com/duct-tape/2013/12/18/perus-rio-maranon-another-grand-canyon/